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EP2135080A4 - Functional arrays for high throughput characterization of regulatory elements in untranslated regions of genes - Google Patents

Functional arrays for high throughput characterization of regulatory elements in untranslated regions of genes

Info

Publication number
EP2135080A4
EP2135080A4 EP08726512A EP08726512A EP2135080A4 EP 2135080 A4 EP2135080 A4 EP 2135080A4 EP 08726512 A EP08726512 A EP 08726512A EP 08726512 A EP08726512 A EP 08726512A EP 2135080 A4 EP2135080 A4 EP 2135080A4
Authority
EP
European Patent Office
Prior art keywords
genes
high throughput
regulatory elements
untranslated regions
throughput characterization
Prior art date
Legal status (The legal status is an assumption and is not a legal conclusion. Google has not performed a legal analysis and makes no representation as to the accuracy of the status listed.)
Withdrawn
Application number
EP08726512A
Other languages
German (de)
French (fr)
Other versions
EP2135080A2 (en
Inventor
Nathan Trinklein
Shelley Force Aldred
Current Assignee (The listed assignees may be inaccurate. Google has not performed a legal analysis and makes no representation or warranty as to the accuracy of the list.)
SwitchGear Genomics
Original Assignee
SwitchGear Genomics
Priority date (The priority date is an assumption and is not a legal conclusion. Google has not performed a legal analysis and makes no representation as to the accuracy of the date listed.)
Filing date
Publication date
Application filed by SwitchGear Genomics filed Critical SwitchGear Genomics
Publication of EP2135080A2 publication Critical patent/EP2135080A2/en
Publication of EP2135080A4 publication Critical patent/EP2135080A4/en
Withdrawn legal-status Critical Current

Links

Classifications

    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12N—MICROORGANISMS OR ENZYMES; COMPOSITIONS THEREOF; PROPAGATING, PRESERVING, OR MAINTAINING MICROORGANISMS; MUTATION OR GENETIC ENGINEERING; CULTURE MEDIA
    • C12N15/00—Mutation or genetic engineering; DNA or RNA concerning genetic engineering, vectors, e.g. plasmids, or their isolation, preparation or purification; Use of hosts therefor
    • C12N15/09—Recombinant DNA-technology
    • C12N15/10—Processes for the isolation, preparation or purification of DNA or RNA
    • C12N15/1034—Isolating an individual clone by screening libraries
    • C12N15/1086—Preparation or screening of expression libraries, e.g. reporter assays
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12N—MICROORGANISMS OR ENZYMES; COMPOSITIONS THEREOF; PROPAGATING, PRESERVING, OR MAINTAINING MICROORGANISMS; MUTATION OR GENETIC ENGINEERING; CULTURE MEDIA
    • C12N15/00—Mutation or genetic engineering; DNA or RNA concerning genetic engineering, vectors, e.g. plasmids, or their isolation, preparation or purification; Use of hosts therefor
    • C12N15/09—Recombinant DNA-technology
    • C12N15/63—Introduction of foreign genetic material using vectors; Vectors; Use of hosts therefor; Regulation of expression
    • C12N15/67—General methods for enhancing the expression
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12Q—MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS; COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES
    • C12Q1/00—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions
    • C12Q1/68—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions involving nucleic acids
    • C12Q1/6897—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions involving nucleic acids involving reporter genes operably linked to promoters

Landscapes

  • Life Sciences & Earth Sciences (AREA)
  • Health & Medical Sciences (AREA)
  • Genetics & Genomics (AREA)
  • Chemical & Material Sciences (AREA)
  • Engineering & Computer Science (AREA)
  • Organic Chemistry (AREA)
  • Zoology (AREA)
  • Wood Science & Technology (AREA)
  • General Engineering & Computer Science (AREA)
  • Bioinformatics & Cheminformatics (AREA)
  • Biotechnology (AREA)
  • Biomedical Technology (AREA)
  • Biophysics (AREA)
  • General Health & Medical Sciences (AREA)
  • Microbiology (AREA)
  • Physics & Mathematics (AREA)
  • Biochemistry (AREA)
  • Molecular Biology (AREA)
  • Proteomics, Peptides & Aminoacids (AREA)
  • Plant Pathology (AREA)
  • Analytical Chemistry (AREA)
  • Bioinformatics & Computational Biology (AREA)
  • Crystallography & Structural Chemistry (AREA)
  • Immunology (AREA)
  • Measuring Or Testing Involving Enzymes Or Micro-Organisms (AREA)
  • Micro-Organisms Or Cultivation Processes Thereof (AREA)
EP08726512A 2007-03-08 2008-03-05 Functional arrays for high throughput characterization of regulatory elements in untranslated regions of genes Withdrawn EP2135080A4 (en)

Applications Claiming Priority (2)

Application Number Priority Date Filing Date Title
US90572707P 2007-03-08 2007-03-08
PCT/US2008/002995 WO2008112127A2 (en) 2007-03-08 2008-03-05 Functional arrays for high throughput characterization of regulatory elements in untranslated regions of genes

Publications (2)

Publication Number Publication Date
EP2135080A2 EP2135080A2 (en) 2009-12-23
EP2135080A4 true EP2135080A4 (en) 2010-12-01

Family

ID=39742238

Family Applications (1)

Application Number Title Priority Date Filing Date
EP08726512A Withdrawn EP2135080A4 (en) 2007-03-08 2008-03-05 Functional arrays for high throughput characterization of regulatory elements in untranslated regions of genes

Country Status (3)

Country Link
US (1) US20080220983A1 (en)
EP (1) EP2135080A4 (en)
WO (1) WO2008112127A2 (en)

Families Citing this family (18)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
WO2008073303A2 (en) * 2006-12-07 2008-06-19 Switchgear Genomics Transcriptional regulatory elements of biological pathways, tools, and methods
US8420315B2 (en) 2007-08-06 2013-04-16 Orion Genomics Llc Single nucleotide polymorphisms and combinations of novel and known polymorphisms for determining the allele-specific expression of the IGF2 gene
EP2955234A1 (en) * 2009-02-11 2015-12-16 Orion Genomics, LLC Combinations of polymorphisms for determining allele-specific expression of igf2
US8815779B2 (en) * 2009-09-16 2014-08-26 SwitchGear Genomics, Inc. Transcription biomarkers of biological responses and methods
WO2011039289A1 (en) * 2009-09-29 2011-04-07 Protagen Ag Marker sequences for pancreatic cancer diseases, pancreatic carcinoma and use thereof
US9006405B2 (en) 2010-06-10 2015-04-14 SwitchGear Genomics, Inc. Modified renilla luciferase nucleic acids and methods of use
US9879254B2 (en) 2012-01-18 2018-01-30 The General Hosptial Corporation Targeting RNAs to microvesicles
SI3019619T1 (en) 2013-07-11 2021-12-31 Modernatx, Inc. Compositions comprising synthetic polynucleotides encoding crispr related proteins and synthetic sgrnas and methods of use
CA2927254C (en) * 2013-12-30 2023-10-24 Curevac Ag Artificial nucleic acid molecules
EP3415629A1 (en) * 2013-12-30 2018-12-19 CureVac AG Artificial nucleic acid molecules
EP4241784A3 (en) 2014-12-12 2023-11-15 CureVac SE Artificial nucleic acid molecules for improved protein expression
ES2924739T3 (en) * 2015-08-28 2022-10-10 Curevac Ag artificial nucleic acid molecules
WO2017059902A1 (en) * 2015-10-07 2017-04-13 Biontech Rna Pharmaceuticals Gmbh 3' utr sequences for stabilization of rna
WO2019193183A2 (en) * 2018-04-05 2019-10-10 Curevac Ag Novel yellow fever nucleic acid molecules for vaccination
WO2019241684A1 (en) * 2018-06-15 2019-12-19 Massachusetts Institute Of Technology Synthetic 5' utr sequences, and high-throughput engineering and screening thereof
US12188060B2 (en) 2020-05-15 2025-01-07 Crispr Therapeutics Ag Messenger RNA encoding Cas9 for use in genome-editing systems
CN118853659A (en) * 2023-04-14 2024-10-29 深圳瑞吉生物科技有限公司 Nucleic acid for increasing the output of mRNA translation protein and its application
CN117535295B (en) * 2024-01-09 2024-04-26 艾斯拓康医药科技(北京)有限公司 Optimized 3' -UTR sequence and application thereof

Citations (1)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
EP1176196A1 (en) * 2000-07-24 2002-01-30 Message Pharmaceuticals, Inc. Functional genomic screen for post-transcriptional 5' and 3' regulatory elements

Family Cites Families (64)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
US6054270A (en) * 1988-05-03 2000-04-25 Oxford Gene Technology Limited Analying polynucleotide sequences
US5424186A (en) * 1989-06-07 1995-06-13 Affymax Technologies N.V. Very large scale immobilized polymer synthesis
US5871928A (en) * 1989-06-07 1999-02-16 Fodor; Stephen P. A. Methods for nucleic acid analysis
US5800992A (en) * 1989-06-07 1998-09-01 Fodor; Stephen P.A. Method of detecting nucleic acids
US5143854A (en) * 1989-06-07 1992-09-01 Affymax Technologies N.V. Large scale photolithographic solid phase synthesis of polypeptides and receptor binding screening thereof
US5242974A (en) * 1991-11-22 1993-09-07 Affymax Technologies N.V. Polymer reversal on solid surfaces
US5527681A (en) * 1989-06-07 1996-06-18 Affymax Technologies N.V. Immobilized molecular synthesis of systematically substituted compounds
US5744101A (en) * 1989-06-07 1998-04-28 Affymax Technologies N.V. Photolabile nucleoside protecting groups
US5252743A (en) * 1989-11-13 1993-10-12 Affymax Technologies N.V. Spatially-addressable immobilization of anti-ligands on surfaces
DK0604552T3 (en) * 1991-09-18 1997-08-04 Affymax Tech Nv Process for the synthesis of different assemblies of oligomers
US5550215A (en) * 1991-11-22 1996-08-27 Holmes; Christopher P. Polymer reversal on solid surfaces
US5384261A (en) * 1991-11-22 1995-01-24 Affymax Technologies N.V. Very large scale immobilized polymer synthesis using mechanically directed flow paths
US5324633A (en) * 1991-11-22 1994-06-28 Affymax Technologies N.V. Method and apparatus for measuring binding affinity
DE69233087T2 (en) * 1991-11-22 2003-12-24 Affymetrix, Inc. (N.D.Ges.D.Staates Delaware) Process for the production of polymer arrays
DE4138621A1 (en) * 1991-11-25 1993-06-17 Boehringer Ingelheim Int METHOD FOR SCREENING SUBSTANCES WITH MODULATING EFFECT ON A RECEPTACLE-RELATED CELLULAR SIGNAL TRANSMISSION PATH
US5491074A (en) * 1993-04-01 1996-02-13 Affymax Technologies Nv Association peptides
US5837832A (en) * 1993-06-25 1998-11-17 Affymetrix, Inc. Arrays of nucleic acid probes on biological chips
US5858659A (en) * 1995-11-29 1999-01-12 Affymetrix, Inc. Polymorphism detection
US5578832A (en) * 1994-09-02 1996-11-26 Affymetrix, Inc. Method and apparatus for imaging a sample on a device
US5631734A (en) * 1994-02-10 1997-05-20 Affymetrix, Inc. Method and apparatus for detection of fluorescently labeled materials
US6090555A (en) * 1997-12-11 2000-07-18 Affymetrix, Inc. Scanned image alignment systems and methods
DE4407222A1 (en) * 1994-03-04 1995-09-07 Basf Ag Process for the recovery of caprolactam from oligo and / or polymers of caprolactam
EP0758403B1 (en) * 1994-05-05 1998-06-24 Beckman Instruments, Inc. Oligonucleotide repeat arrays
US5571639A (en) * 1994-05-24 1996-11-05 Affymax Technologies N.V. Computer-aided engineering system for design of sequence arrays and lithographic masks
US5807522A (en) * 1994-06-17 1998-09-15 The Board Of Trustees Of The Leland Stanford Junior University Methods for fabricating microarrays of biological samples
US5795716A (en) * 1994-10-21 1998-08-18 Chee; Mark S. Computer-aided visualization and analysis system for sequence evaluation
US5599695A (en) * 1995-02-27 1997-02-04 Affymetrix, Inc. Printing molecular library arrays using deprotection agents solely in the vapor phase
US5624711A (en) * 1995-04-27 1997-04-29 Affymax Technologies, N.V. Derivatization of solid supports and methods for oligomer synthesis
US5888765A (en) * 1995-06-23 1999-03-30 President And Fellows Of Harvard College Endothelial-cell specific promoter
US5968740A (en) * 1995-07-24 1999-10-19 Affymetrix, Inc. Method of Identifying a Base in a Nucleic Acid
US6025901A (en) * 1995-08-14 2000-02-15 Sharp Kabushiki Kaisha Liquid crystal display device and method for producing the same
US6242211B1 (en) * 1996-04-24 2001-06-05 Terragen Discovery, Inc. Methods for generating and screening novel metabolic pathways
JP2000512744A (en) * 1996-05-16 2000-09-26 アフィメトリックス，インコーポレイテッド System and method for detecting label material
WO1998037235A1 (en) * 1997-02-24 1998-08-27 Cornell Research Foundation, Inc. Method of screening agents as candidates for drugs or sources of drugs
WO1999023254A1 (en) * 1997-10-31 1999-05-14 Affymetrix, Inc. Expression profiles in adult and fetal organs
AU746786B2 (en) * 1997-12-08 2002-05-02 California Institute Of Technology Method for creating polynucleotide and polypeptide sequences
GB9801902D0 (en) * 1998-01-29 1998-03-25 Cancer Res Campaign Tech A gene promoter
WO1999049019A2 (en) * 1998-03-27 1999-09-30 Prolume, Ltd. Luciferases, fluorescent proteins, nucleic acids encoding the luciferases and fluorescent proteins and the use thereof in diagnostics
US5936324A (en) * 1998-03-30 1999-08-10 Genetic Microsystems Inc. Moving magnet scanner
EP2253704B1 (en) * 1999-01-19 2015-08-19 Codexis Mayflower Holdings, LLC Oligonucleotide mediated nucleic acid recombination
US6504084B1 (en) * 1999-04-23 2003-01-07 Pioneer Hi-Bred International, Inc. Maize NPR1 polynucleotides and methods of use
US6630324B1 (en) * 1999-07-29 2003-10-07 Baylor College Of Medicine Aldehyde reductase bidirectional promoter and its use
US6605431B1 (en) * 1999-08-17 2003-08-12 Wisconsin Alumni Research Foundation Promoter elements and methods of use
US20020006664A1 (en) * 1999-09-17 2002-01-17 Sabatini David M. Arrayed transfection method and uses related thereto
US6544790B1 (en) * 1999-09-17 2003-04-08 Whitehead Institute For Biomedical Research Reverse transfection method
US7468275B2 (en) * 2000-01-28 2008-12-23 The Scripps Research Institute Synthetic internal ribosome entry sites and methods of identifying same
US20030125246A9 (en) * 2000-01-31 2003-07-03 Rosen Craig A. Nucleic acids, proteins, and antibodies
WO2001084155A1 (en) * 2000-04-28 2001-11-08 Message Pharmaceuticals, Inc. Methods for identifying novel nucleic acid regulatory elements and compounds that affect the regulation
JP2004512029A (en) * 2000-08-16 2004-04-22 カイロン　コーポレイション Human genes and gene expression products
US7067649B2 (en) * 2000-11-17 2006-06-27 Vascular Biogenics Ltd. Promoters exhibiting endothelial cell specificity and methods of using same
US7060459B2 (en) * 2000-12-08 2006-06-13 Juan Saus TNF-inducible promoters and methods for using
AU2002241154A1 (en) * 2001-03-21 2002-10-03 Isis Innovation Ltd. Assays, methods and means relating to hypoxia inducible factor (hif) hydroxylase
US20040219543A1 (en) * 2001-04-02 2004-11-04 Ralph Wirtz Method for specifically detecting, isolating and characterizing cells from body samples by transfecting nucleic acid constructs
US6821737B2 (en) * 2001-06-08 2004-11-23 Panomics, Inc. Method for screening for drug candidates for modulating transcription factor activity
US6670129B2 (en) * 2001-09-24 2003-12-30 Corning Incorporated Cell transfection apparatus and methods for making and using the cell transfection apparatus
EP1438416A4 (en) * 2001-09-26 2007-09-05 Epigenx Pharmaceutical Inc Assays for dna methylation changes
US20030211481A1 (en) * 2002-05-08 2003-11-13 Erives Albert J. Method for identifying cellular targets
WO2004039394A1 (en) * 2002-10-25 2004-05-13 Genentech, Inc. Novel composition and methods for the treatment of immune related diseases
US7022481B2 (en) * 2002-12-19 2006-04-04 Rosetta Inpharmatics Llc Methods of using glucan synthase pathway reporter genes to screen for antifungal compounds
CA2517235A1 (en) * 2003-02-27 2004-09-10 Nucleonics Inc. Methods and constructs for evaluation of rnai targets and effector molecules
US20050074827A1 (en) * 2003-07-18 2005-04-07 Ute Muh Methods for identifying modulators of quorum-sensing signaling in bacteria
US20070072175A1 (en) * 2005-05-13 2007-03-29 Biogen Idec Ma Inc. Nucleotide array containing polynucleotide probes complementary to, or fragments of, cynomolgus monkey genes and the use thereof
US20070161031A1 (en) * 2005-12-16 2007-07-12 The Board Of Trustees Of The Leland Stanford Junior University Functional arrays for high throughput characterization of gene expression regulatory elements
WO2008073303A2 (en) * 2006-12-07 2008-06-19 Switchgear Genomics Transcriptional regulatory elements of biological pathways, tools, and methods

Patent Citations (1)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
EP1176196A1 (en) * 2000-07-24 2002-01-30 Message Pharmaceuticals, Inc. Functional genomic screen for post-transcriptional 5' and 3' regulatory elements

Non-Patent Citations (4)

* Cited by examiner, † Cited by third party
Title
DAVULURI RAMANA V ET AL: "CART classification of human 5' UTR sequences", November 2000, GENOME RESEARCH, VOL. 10, NR. 11, PAGE(S) 1807-1816, ISSN: 1088-9051, XP002605204 *
KAMURA N ET AL: "Selection of 5'-untranslated sequences that enhance initiation of translation in a cell-free protein synthesis system from wheat embryos", BIOORGANIC & MEDICINAL CHEMISTRY LETTERS, PERGAMON, ELSEVIER SCIENCE, GB LNKD- DOI:10.1016/J.BMCL.2005.09.013, vol. 15, no. 24, 15 December 2005 (2005-12-15), pages 5402 - 5406, XP025314213, ISSN: 0960-894X, [retrieved on 20051215] *
KANAMORI H ET AL: "DIFFERENTIAL DISPLAY COMBINED WITH A REGULATED TRANSIENT EXPRESSIONSYSTEM", BIOTECHNIQUES, INFORMA LIFE SCIENCES PUBLISHING, WESTBOROUGH, MA, US, vol. 26, no. 6, 1 June 1999 (1999-06-01), pages 1018 - 1020, XP000851412, ISSN: 0736-6205 *
TRINKLEIN NATHAN D ET AL: "Identification and functional analysis of human transcriptional promoters", GENOME RESEARCH, COLD SPRING HARBOR LABORATORY PRESS, WOODBURY, NY, US LNKD- DOI:10.1101/GR.794803, vol. 13, no. 2, 1 February 2003 (2003-02-01), pages 308 - 312, XP009126139, ISSN: 1088-9051 *

Also Published As

Publication number Publication date
US20080220983A1 (en) 2008-09-11
EP2135080A2 (en) 2009-12-23
WO2008112127A2 (en) 2008-09-18
WO2008112127A3 (en) 2008-11-13

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